computePrunedPCARef: Compute principal component axes (PCA) on pruned SNV with the...

In belleau/aicsPaper: Accurate Inference of Genetic Ancestry from Cancer Sequencing

Compute principal component axes (PCA) on pruned SNV with the reference samples

Description

This function compute the PCA on pruned SNV with the reference samples

Usage

computePrunedPCARef(gds, listRef, np = 1L)

Arguments

gds	an object of class SNPRelate::SNPGDSFileClass, a SNP GDS file.
listRef	a vector of string representing the identifiant of the samples in the reference (unrelated).
np	a single positive integer representing the number of threads. Default: 1L.

Details

More information about the method used to calculate the patient eigenvectors can be found at the Bioconductor SNPRelate website: https://bioconductor.org/packages/SNPRelate/

Value

listPCA a list containing two objects pca.unrel -> snpgdsPCAClass and a snp.load -> snpgdsPCASNPLoading

Author(s)

Pascal Belleau, Astrid Deschênes and Alexander Krasnitz

Examples

## Path to the demo pedigree file is located in this package
data.dir <- system.file("extdata", "RAIDS")

## TODO

belleau/aicsPaper documentation built on Aug. 4, 2022, 1:12 a.m.